In Part 1, I recounted how Darwinists are deeply invested in the rhetorical value of the emotional argument that humans and chimps have a 98% - 99% genetic similarity. Anthropologist John Marks reports that sometimes Darwinists even use this statistic to contend that our lives are "meaningless"! To explore this debate, I recently blogged about a Science news article entitled "Relative Differences: The Myth of 1%" that reported that the 1% human/chimp genetic difference statistic was a "myth," because "studies are showing that [humans and chimps] are not as similar as many tend to believe." The Science news article reported that improved genome comparison modeling methods indicate that humans and chimps are "6.4%" genetically distinct from one another.

Apparently my discussion of the Science news article concerned its author, Jon Cohen, whose e-mail response to me I also posted in full in Part 1. Oddly, Mr. Cohen's response backpedals and promotes the importance of the 1% human/chimp genetic-difference statistic--despite the fact that his Science article had forcefully emphasized the decreasing importance of that statistic. Perhaps he wasn't quite ready to share any of the responsility for Darwinists losing their rhetorical investment in the 1% statistic. I now publish my response to Mr. Cohen below. I hope that this exchange not only provides an educational object lesson to readers regarding the quality of counter-arguments from the Darwinian science-writing community, but also helps readers understand why the 1.23% human/chimp genetic difference statistic is not all it appears to be. Here is my reply to Mr. Cohen:

Dear Mr. Cohen,

Greetings and thank you for e-mailing me about your concerns, and for also passing on many articles pertinent to this subject. I think it's best to start this off by saying that I saw your bio on the AAAS website that noted that you are a UCSD graduate who lives in San Diego county. In light of the tragic fires that are currently threatening many in San Diego, I wanted to say that I hope the best for you and your family and I hope you are safe tonight.

Regarding your e-mail, when I read the subject of your e-mail, "Errors in your posting," I expected your e-mail to document actual errors in my posting. Instead, I merely found you making accusations against me that I "selectively and out of context" "fail to scrutinize what the original reports," and that I am "sloppy, inaccurate, and overtly biased." These assorted accusations sound serious, and if they proved true, of course I would be concerned and I would want to issue some correction. But in fact your accusations were not backed up by anything you said in your e-mail.

Please allow me to discuss your concerns below.

Concern 1. You wrote that "our genes--in contrast to what the Scientific American posting states--are only 1.23% different" (emphasis yours). My post never said otherwise, but your implication is that I should have devoted my post to pushing the 1% DNA sequence-difference statistic rather than the 6.4% gene-copy difference statistic. But my post was reporting on yourScience news article, and the Scientific American blog post, and since those two sources dealt primarily with emphasizing the importance gene copy percent similarities between humans and chimps rather than DNA-sequence differences, my post dealt with gene copy percent differences between humans and chimps. Thus, I focused on quoting those sources where those sources stated, "human and chimpanzee gene copy numbers differ by a whopping 6.4%" and "humans may have as little as 99% of their genes in common with one another, and, by the same analysis, as little as 95% of their genes in common with chimpanzees."

Your e-mail seems to imply that you feel I should have promoted the 1% human/chimp DNA-sequence difference statistic as the more important figure, but in fact I was simply following the approach you took in your Science news article where you printed the following descriptions about the 1% DNA-sequence difference statistic:

"myth"

"truism [that] should be retired"

"more a hindrance for understanding than a help"

"the 1% difference wasn't the whole story."

"studies are showing that they are not as similar as many tend to believe"

To respond directly to your concern, my post never stated nor implied that the 1% figure was itself incorrect in its context. Rather, I followed your approach by quoting you calling it a "myth" or by characterizing it as "becoming a thing of the past" (following you when you suggested it may be a "truism [that] should be retired" or quoting a scientist who called it "more a hindrance for understanding than a help". To reiterate: I never said that the 1% figure was itself incorrect, I just implied that it is becoming irrelevant due to more important statistical methods of comparison related to gene copy number--doing my best to convey to our readers the message of your article.

I do not see any grounds for complaint on your part regarding my treatment of this matter since I was essentially following the very approach you took in your article. In fact, I find it ironic that you are now emailing me promoting the importance of the 1% sequence difference statistic when in fact your article calls that 1% statistic a "myth," a "truism [that] should be retired," a "hindrance for understanding," not "the whole story," etc. Is the author of the "Myth of 1%" article is now trying to promote that same 1% myth after Discovery Institute blogged about your article and observed that humans and chimps "are not as similar as many tend to believe"? Your e-mail to me comes off like backpedaling.

Concern 2. You wrote: "You also state that my article 'reports' that copy numbers differ by 6.4%. Not only does this misleadingly imply that humans thus differ from chimps by 6.4% (it's probably closer to 5%), you fail to note that my article was not the source of this figure: I was citing a report that was done by a computational genomics researcher."

Regarding your charge that I imply that your article was the source of the 6.4% statistic, observe that my original blog post stated that your article was a "Science news article" that "reported" that gene copy numbers differed by 6.4% between humans and chimps. No informed reader would take your article as the original research source for that statistic, but rather they would take it precisely how I described it: a Science news source reporting on other research. To learn about the original source, the reader could look up your article (which my post links to). I find it ironic that you are criticizing me for doing exactly what you did: I quoted a source discussing the 6.4% research finding, and I noted my source.

Regarding your charge that gene copy similarity differs by 5% rather than 6.4%, and that I used the wrong statistical percentage, I first note that I quoted the Scientific American post where it stated that "humans may have ... as little as 95% of their genes in common with chimpanzees." 95% "in common" of course equals a 5% difference, so the 5% approximation seems present in the quote I provided from Scientific American.

But there deeper problem with this complaint: you claim that my post is "misleading" because you say the 6.4% statistic is "probably closer to 5%". Yet I am perplexed at how you complain to me here, because when I stated the 6.4% difference, I was simply quoting your article, and your article never says anything about a 5% gene copy difference statistic and in fact the statistic you give is 6.4%. If the 6.4% statistic is in error, then your article is the source of that error because my post directly quoted your article! It seems that you accuse me of propagating an error when I was just quoting you. If it was in error, have you corrected it publicly? If so, I'd be happy to update my post accordingly.

Here you employ an unfortunate example of Darwinian moral logic: I quote a pro-evolution science reporter, and then that pro-evolution science reporter claims that his statement was off by ~1.4% and accuses me of propagating an error by quoting him. Such Darwinian moral logic is incredible, but it does have a simple and clear-cut rule: if a Darwinist is wrong, it must be an ID guy's fault.

Concern 3. You wrote: "The 1.23% is a hard fact: It's based on sequencing the entire human genome and the chimpanzee genome" (emphasis yours). I'm more than willing to believe you when you wrote "The 1.23% is a hard fact" -- and as I noted above, I never claimed that the statistic was wrong. To repeat, the only language I used to describe the 1% statistic was language that you yourself used in your article (i.e. "Myth") or characterizing it how you did (i.e. "truism should be retired"), etc. Nonetheless, despite your article's emphatic diminution of the importance of the 1% statistic, I am more than willing to accept that the 1.23% sequence difference statistic "is a hard fact." But I do have some comments in this regard:

In fact, the distinction between (i) the 6.4% difference in non-coding DNA and gene-copy number and (ii) 1.23% difference between the gene sequences is not one of estimate versus "hard fact," but rather represents different kinds of estimates. The 1.23% difference is every bit as much an estimate as the 6.4%. For example, the 1.23% comes from sequence alignments that were performed only when homologous genes were available from both genomes. Indeed, your Science news article concedes this fact, as it admits that "the figure reflects only base substitutions, not the many stretches of DNA that have been inserted or deleted in the genomes." What do you do when the chimp genome has no homologue to a human gene or non-coding DNA sequence? Do you add all those residues to the error column? No, you ignore them altogether. So the 1.23% is not really a "hard fact," unless you are careful to so caveat the result: it ignores insertions and deletions ("indels"), especially genes that are present in one species but absent in the other.

Given that (quite large) caveat then yes, the 1.23% figure probably has much less uncertainty than the 6.4% figure. But given that the 1.23% statistic requires such a weighty caveat (your article admits that the indels may account for up to 3% differences between the two genomes -- more than twice as great as the 1.23% difference statistic itself!), one is not unjustified in holding skepticism towards claims that the 1.23% statistic is really all that impressive or meaningful.

There is also the problem that the 1.23% value does not have a lot of meaning since there is quite a bit of variance between genes. Many human-chimp gene comparisons show identical or near identical alignments, but so do some human-banana alignments. More importantly, certain types of human-chimp alignments show substantial differences, but the 1.23% statistic averages over all of them. Yes, it provides an overall average value which might be helpful when merely comparing different genomes, but given the all-important caveats, its importance is dubious.

In the end, it seems like you are now backpedaling by stridently promoting the 1% similarity statistic to me in your e-mail, calling it a "hard fact" when you yourself reported in your article that it was a "myth," suggested it may be a "truism [that] should be retired," quoted a scientist calling it "more a hindrance for understanding than a help," and reported it "wasn't the whole story," etc. Regardless, the wording I used in my blog post simply followed the wording of your article, so if there is any error here, it cannot be attributed to me for following the approach you took in your Science news article.

Concern 4. You wrote: "The claim that humans are as different from each other as was previously thought we were different from chimps also is misleading and inaccurate." Regarding this complaint, I was simply quoting the Scientific American article when it stated, "Humans turn out to be as genetically different from one another as it was previously thought they were different from chimps." If you take issue with that claim, then again I have 2 questions:

(1) Did you e-mail the author of the Scientific American post, the original source for that claim, to state your objections?
(2) If not, why not?

Again, I was simply quoting a science news source, Scientific American. If their source was in error, I would love to know about it so I can make it clear to our readers that Scientific American was wrong. But it seems to me that if you have concerns, you need to take the issue up with them, as they are the ones who said it.

Again, I see an astounding type of Darwinian moral logic at work here: if a Darwinist is wrong, it must be an ID guy's fault. I'll be happy to correct anything if Scientific American posts any changes on this matter.

Concern 5. You observe that "None of the original studies I cited in my article or Venter's genome paper suggest in any way that their findings challenge Darwinian evolution, and I doubt that any of those researchers would support that conclusion from their data." In response I ask you, where did I state that any of these papers "challenge Darwinian evolution"? I am simply discussing a scientific debate of interest to our readers, namely the degree of genetic similarity between humans and chimps, and my post made no conclusions about the validity of Darwinian evolution. Again, I see no error, but you're putting words in my mouth that I simply did not state. In fact, I specifically stated that biologists will have to sort out the implications of these data, as I wrote: "The implications of these differences remain to be sorted out by biologists."

Concern 6. You wrote: "The bottom line is that your post is so distant from the sources that you have completely garbled the data to support Intelligent Design." I've already established that I followed the sources I quoted accurately and that I myself did not "garble" anything. But here's the more pertinent question: where did I state that any of these papers "support intelligent design"? I am simply discussing a scientific debate of interest to our readers, namely the degree of genetic similarity between humans and chimps, and my post made no conclusions about the validity of intelligent design.

Again, I see no error, but you seem to be putting words in my mouth that I did not state. And I reiterate that my post specifically remained neutral on the issue of larger implications of these data by stating "The implications of these differences remain to be sorted out by biologists."

This now raises a question, what are the implications of these findings? As your piece discussed, these comparisons have been raised by evolutionists, and evolutionists have claimed these comparisons as powerful evidence for the theory. Subsequent modification and elaboration on these data are naturally going to be of interest to our readers, even if hard and fast conclusions are not immediately obvious.

We might reasonably ask the evolutionist why the 1% difference value was considered to be such powerful evidence for Darwinian evolution, and at what point does the comparison cease to support Darwinian evolution? 2%? 3%? 6.4%? 10%? Is there an objective metric for falsification here?

Of course there are no answers to these questions, because the reasoning behind the claim that 1% difference was powerful evidence for evolution was never elucidated in the first place. This is why I wrote:

From a technical scientific perspective, the degree of genetic similarity between humans and chimps seems to be of questionable relevance when one is trying to determine whether two species share a Darwinian past. After all, designers regularly re-use parts that work, especially programming components, so there's no reason to presume that mere genetic similarity necessarily implies common descent over common design. Moreover, even if such genetic similarities were to imply common ancestry, they don't demonstrate a plausible stepwise Darwinian evolutionary pathway.

Your insistence that the evolutionists find no problem with these newer data is no surprise. But this hardly means the data are of no interest.

Conclusion
You wrote: "You are welcome to post my e-mail in its entirety, but given the errors that you made in your post by selectively quoting from other posts, please do not excerpt this for a public posting."

I appreciate your kind offer. As you identified no errors in my post (#s 1-6); made accusations against me which are much more strongly applicable against you given that I was simply following your approach (#s 1-3); accused me of making errors when in reality, if there are errors, then those are the errors of authorities whom I quoted and not errors on my part (#s 2 & 4); and finally falsely accused me of saying things I never said (#s 5-6); the only reason I think it would be worth responding publicly would be to show people your apparent backpedaling, and to reveal the quality of your objections. But I can assure you that if I do choose to respond, I will most certainly respect your request and I will post your reply to me in its entirety.

Finally, to end on a friendly personal note, I'm also a UCSD alum and I lived in San Diego for many years. In fact I spent much time yesterday checking on my friends in San Diego in light of the fire (some of whom are still waiting to see if their homes survive). One of my friends, like you, lives in Cardiff by the Sea, and his family has evacuated to Los Angeles. So I wish you and your family safety, health, and peace during this time.

If you have time to reply, I look forward to any answers you may have to my questions. Thank you for your time.